In order to operate on fat bundles Apple provides a utility called lipo.

If you are in a situation where you are limited by processor architecture – for example, if you never expect to use internal hard drive of your iBook in firewire target mode to boot up an i386 system – it is possible to remove the extra “fat” from fat binaries, to save some disk space.

A quick test confirms that Terminal.app continues to run as before, however to make sure that everything is kosher I would probably want to correct permissions on the new binary to match what it was on the original.

Disk space saving will not be big, as an average .app consists of many other objects besides the executable itself, so this is probably not a very big issue. If one tries to remove a non-existing architecture from a binary, lipo will complain: